Query 046293
Match_columns 695
No_of_seqs 288 out of 1232
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 10:35:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046293.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046293hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 7E-121 1E-125 1039.4 58.5 617 20-653 67-762 (846)
2 PF03101 FAR1: FAR1 DNA-bindin 99.8 2.4E-19 5.2E-24 154.2 8.1 89 41-129 1-91 (91)
3 PF10551 MULE: MULE transposas 99.7 3.4E-17 7.4E-22 141.4 7.9 79 214-294 1-93 (93)
4 PF08731 AFT: Transcription fa 99.3 3.6E-11 7.7E-16 102.7 9.8 88 33-127 1-111 (111)
5 smart00575 ZnF_PMZ plant mutat 98.9 4.5E-10 9.7E-15 73.0 2.1 26 473-498 2-27 (28)
6 PF00872 Transposase_mut: Tran 98.9 3.6E-10 7.8E-15 122.7 0.2 171 208-380 163-350 (381)
7 PF03108 DBD_Tnp_Mut: MuDR fam 98.7 5.2E-08 1.1E-12 78.3 8.3 66 24-116 1-67 (67)
8 PF04434 SWIM: SWIM zinc finge 98.3 7.6E-07 1.7E-11 63.5 3.2 28 469-496 12-39 (40)
9 COG3328 Transposase and inacti 97.6 0.00035 7.5E-09 75.0 10.4 167 208-381 146-330 (379)
10 PF03106 WRKY: WRKY DNA -bindi 93.4 0.39 8.4E-06 37.4 6.8 56 50-126 3-59 (60)
11 PF15288 zf-CCHC_6: Zinc knuck 93.3 0.044 9.5E-07 38.3 1.3 22 631-654 2-25 (40)
12 PF00098 zf-CCHC: Zinc knuckle 93.3 0.065 1.4E-06 30.8 1.8 18 631-650 1-18 (18)
13 PF00665 rve: Integrase core d 89.6 1.9 4E-05 38.1 8.3 75 207-282 6-81 (120)
14 PF04684 BAF1_ABF1: BAF1 / ABF 86.4 1.5 3.3E-05 47.4 6.3 56 29-110 24-79 (496)
15 COG5179 TAF1 Transcription ini 85.0 0.49 1.1E-05 52.5 1.9 28 625-654 932-961 (968)
16 smart00774 WRKY DNA binding do 84.1 2.2 4.9E-05 33.0 4.6 55 51-125 4-59 (59)
17 PF13696 zf-CCHC_2: Zinc knuck 83.4 0.56 1.2E-05 31.3 0.9 23 628-652 6-28 (32)
18 PF04500 FLYWCH: FLYWCH zinc f 77.4 3.8 8.2E-05 31.5 4.1 25 98-125 38-62 (62)
19 PF14392 zf-CCHC_4: Zinc knuck 67.0 2.4 5.2E-05 31.5 0.6 20 629-650 30-49 (49)
20 smart00343 ZnF_C2HC zinc finge 66.9 3.1 6.6E-05 26.2 1.0 18 632-651 1-18 (26)
21 PF13610 DDE_Tnp_IS240: DDE do 65.5 1.9 4.1E-05 39.9 -0.2 70 207-280 1-70 (140)
22 PHA02517 putative transposase 61.0 34 0.00075 35.3 8.3 74 207-282 110-183 (277)
23 PF04937 DUF659: Protein of un 53.7 1.5E+02 0.0033 27.8 10.4 97 200-299 26-138 (153)
24 PRK14702 insertion element IS2 37.7 1.3E+02 0.0029 30.9 8.0 72 207-279 87-163 (262)
25 PRK09409 IS2 transposase TnpB; 34.7 1.7E+02 0.0037 30.8 8.4 72 207-279 126-202 (301)
26 PF13917 zf-CCHC_3: Zinc knuck 34.7 26 0.00056 25.1 1.5 19 630-650 4-22 (42)
27 COG4279 Uncharacterized conser 34.3 22 0.00047 35.8 1.5 24 471-497 124-147 (266)
28 KOG0341 DEAD-box protein abstr 29.1 26 0.00057 37.5 1.1 24 629-654 569-592 (610)
29 COG5431 Uncharacterized metal- 27.0 58 0.0013 28.1 2.6 27 461-493 45-76 (117)
30 PF01610 DDE_Tnp_ISL3: Transpo 26.6 1.1E+02 0.0024 30.8 5.3 85 210-300 1-99 (249)
31 PF11433 DUF3198: Protein of u 25.5 1.7E+02 0.0036 21.5 4.2 44 308-352 6-49 (51)
32 PF12762 DDE_Tnp_IS1595: ISXO2 23.9 2.1E+02 0.0045 26.3 6.2 50 226-280 36-86 (151)
33 PF04800 ETC_C1_NDUFA4: ETC co 22.6 75 0.0016 27.6 2.5 28 29-60 51-78 (101)
34 PF05741 zf-nanos: Nanos RNA b 21.1 33 0.00071 26.2 0.1 21 629-651 32-55 (55)
35 PF14201 DUF4318: Domain of un 21.0 2.5E+02 0.0054 22.9 5.1 28 32-59 13-40 (74)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=6.6e-121 Score=1039.40 Aligned_cols=617 Identities=30% Similarity=0.517 Sum_probs=525.1
Q ss_pred cccCCCCCCCCCccCCHHHHHHHHHHHhhhcCcEEEEecccccccCCceeEEEEEEccCCccccccc-cc----------
Q 046293 20 EVALNRKPHKGKKFDTLDDAYEFYKKYAKEGGFSIQINSSKICKESNDIIRKEYVCFKEGQARQSKV-VN---------- 88 (695)
Q Consensus 20 ~~~~~~~p~~g~~F~S~eea~~~y~~yA~~~GF~i~~~~s~~~k~~g~~~~~~~~C~r~G~~~~~~~-~~---------- 88 (695)
+.+...+|.+||+|+|+|||++||+.||+..||+||+.++++++.+|.++.++|+|+|+|+++.+.. .+
T Consensus 67 ~~~~~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~ 146 (846)
T PLN03097 67 KEDTNLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQD 146 (846)
T ss_pred cCCCCccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccC
Confidence 4466789999999999999999999999999999999999988888999999999999998764321 00
Q ss_pred --cccccc-ccccCceeEEEEEEeeCceEEEEEEeecccCCCCCccccccccccCCCcHHHh-----------------h
Q 046293 89 --RKRRRG-IIRGGCSANLVVVKYEFGKYMVRIFVEEHNHTLSSPRMVHLLRSHRSMSAVQK-----------------S 148 (695)
Q Consensus 89 --~~r~~~-~~r~gC~a~i~~~~~~~~~w~v~~~~~~HNH~l~~~~~~~~l~s~r~~~~~~~-----------------~ 148 (695)
..+++| .+|+||||+|++++.++|+|+|+.|+.+|||+|.++..+.. +..+.+....+ .
T Consensus 147 ~~~~~~rR~~tRtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~~~~~~-~~r~~~~~~~~~~~~~~~v~~~~~d~~~~ 225 (846)
T PLN03097 147 PENGTGRRSCAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPAQAVSE-QTRKMYAAMARQFAEYKNVVGLKNDSKSS 225 (846)
T ss_pred cccccccccccCCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCccccch-hhhhhHHHHHhhhhccccccccchhhcch
Confidence 011234 68999999999999779999999999999999987653221 11111111100 1
Q ss_pred HH--HHhhccCCCHHHHHHHHHHhhhcCCCcEEEEEeccCCceeEEEEccccchHHHhhCCcEEEEecccccCCCCCcee
Q 046293 149 LS--QQLAAVNIPTYILYEHFQSEKEKNSSFFYNIKAGCDDRITHCFWADAICRRAYKFYGDVIVFDTTYNTNRYNMIFA 226 (695)
Q Consensus 149 L~--rr~~~~~~d~~~l~~~l~~~~~~np~f~~~~~~d~~~~l~~ifw~~~~~~~~~~~f~dVl~iD~Ty~tn~y~~pL~ 226 (695)
+. |++.+..+|+++|++||++++.+||+|||++++|++|+|++|||+|+.|+.+|.+|||||+||+||+||+|+|||+
T Consensus 226 ~~~~r~~~~~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y~~FGDvV~fDTTY~tN~y~~Pfa 305 (846)
T PLN03097 226 FDKGRNLGLEAGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDYGNFSDVVSFDTTYVRNKYKMPLA 305 (846)
T ss_pred hhHHHhhhcccchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHHHHHHHhcCCEEEEeceeeccccCcEEE
Confidence 11 3356788999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHHh-----------hhhHHHHHHHHHH
Q 046293 227 PFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMIL-----------HLAYWHILNKFLE 295 (695)
Q Consensus 227 ~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~~-----------~lC~~Hi~~n~~~ 295 (695)
+|+|+|||+|+++|||||+.+|+.|+|.|||++|+++|+|+.|.+||||+|.+|.+ |+|.|||++|+.+
T Consensus 306 ~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiTDqd~am~~AI~~VfP~t~Hr~C~wHI~~~~~e 385 (846)
T PLN03097 306 LFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKVIITDQDKAMKSVISEVFPNAHHCFFLWHILGKVSE 385 (846)
T ss_pred EEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEecCCHHHHHHHHHHCCCceehhhHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999987 9999999999999
Q ss_pred hhhhhccccc--HHHHHHHHhhcCChHHHHHHHHHHHHHhccchhHHHHHHHHhhccchhhhhccccccCccccCcccch
Q 046293 296 RLSKTVHTEN--YRHFQKCIWESNTIEKFDALWKDVIDKAKLIENEWLQGVYEIRSKWVHAYVNHVFSAGMSSSNRAESN 373 (695)
Q Consensus 296 ~~~~~~~~~~--~~~~~~~v~~~~t~~eFe~~w~~l~~~~~~~~~~~l~~l~~~re~Wa~ay~~~~~~~g~~tt~r~Es~ 373 (695)
+++..+...+ ..+|.+||+.+++++|||..|..|+++|++++|+||+.||+.|++||+||+++.|++||.||+|+||+
T Consensus 386 ~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~k~~F~agm~sTqRSES~ 465 (846)
T PLN03097 386 NLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYMRDAFLAGMSTVQRSESI 465 (846)
T ss_pred HhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHhcccccCCcccccccccH
Confidence 9999876554 88999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHH-----------------HHHHHHHHHHHHHHhhhhhhcCCcccccchHHHHHHHhhcChHHHHHHHHHHHHhhcccE
Q 046293 374 HAI-----------------FRRALSQQRHEELIADNKDLNERPMLRLPLQIEKKMSEIYTCEIFYIFQDELWNSLLHAI 436 (695)
Q Consensus 374 n~~-----------------~~~~l~~~~~~e~~~d~~~~~~~~~~~~~~~~e~q~~~~yT~~vf~~~q~el~~s~~~~v 436 (695)
|++ |+++++.++++|+++|+.+.++.|.+++++|||+||+++|||+||++||+|+..+..|.+
T Consensus 466 Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~iF~kFQ~El~~~~~~~~ 545 (846)
T PLN03097 466 NAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHAVFKKFQVEVLGAVACHP 545 (846)
T ss_pred HHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHHHHHHHHHHHHHHhhheEE
Confidence 998 678889999999999999999999999999999999999999999999999999999988
Q ss_pred EEEeecCceeEEEEEeecCCccceEEEEEecCcceEEeeecccccCCCchhhHHHHHHHcCcccCCccchhhhhhhcccc
Q 046293 437 ELVKENEDCLVYNVVNQEDGVSKVFEVLYDKKLDFVSCICKKFKSEGIPCTHMLALFKKLQISFMPNIYILKRWTKAAKL 516 (695)
Q Consensus 437 ~~~~~~~~~~~y~V~~~~~~~~k~~~V~~d~~~~~~tCsC~~~q~~GiPC~H~l~vl~~~~~~~iP~~yI~~RWtk~ak~ 516 (695)
....++|...+|.|...+..++ |+|.+|.....++|+|++|++.||||+|||+||.++++.+||++||++||||+|+.
T Consensus 546 ~~~~~dg~~~~y~V~~~~~~~~--~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~IP~~YILkRWTKdAK~ 623 (846)
T PLN03097 546 KMESQDETSITFRVQDFEKNQD--FTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAIPSQYILKRWTKDAKS 623 (846)
T ss_pred eeeccCCceEEEEEEEecCCCc--EEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccCchhhhhhhchhhhhh
Confidence 8887888889999987655455 99999999999999999999999999999999999999999999999999999998
Q ss_pred ccccCCCCcccCCCCCchHHHHHHHHHc---------ccCHHHHHHHHHHHHHHH-HHhhhhhHHHHh-hhhhhcccccC
Q 046293 517 ERVMDRDGVEINDCSNKSILLRRTKLFQ---------FTSNVIDKVVLSEVASEI-VIENLEDALEKV-KLVMESCRSEG 585 (695)
Q Consensus 517 ~~~~d~~~~~~~~~~~~~~~~r~~~L~~---------~~s~e~y~~a~~~l~~~~-~~~~~~~~~~~~-~~~~~~~~~e~ 585 (695)
..+.+.. .....+.++||+.|++ +.|+|.|+.|+++|++++ ....+++....+ ..+ .-
T Consensus 624 ~~~~~~~-----~~~~~~~~~Ryn~L~r~a~kla~~as~S~E~y~~a~~~L~e~~~~~~~~~n~~~~~~~~~------~~ 692 (846)
T PLN03097 624 RHLLGEE-----SEQVQSRVQRYNDLCQRALKLSEEASLSQESYNIAFRALEEAFGNCISMNNSNKSLVEAG------TS 692 (846)
T ss_pred cccCccc-----cccccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhccCCCccccc------cc
Confidence 6665542 1224567899999998 689999999999999997 333333322111 010 00
Q ss_pred ccccccCCCCC---ccCCCccc-ccCCCCCCCCCChhh-hhHhhcCCCCcccCCCCCCCCCCCCCCCCcchhh
Q 046293 586 VLEKNSGMQQP---HFNEPLQI-RAKGCGKRLKGGKEK-AKEKAKGKDKGRRCNGCGLVGQSHDKRNCPLLIK 653 (695)
Q Consensus 586 ~~~~~~~~~~~---~v~~P~~~-r~kGRpkr~k~~~e~-~~~~~~~~kr~~~C~~C~~~~~GHn~~tCp~~~~ 653 (695)
...-.++.+.. ...+|..+ ++++++++..+..|. +.+.+ ..+++-|..|++ ..+|+...||..+-
T Consensus 693 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~-~~~~d~~y~~q~~~ 762 (846)
T PLN03097 693 PTHGLLCIEDDNQSRSMTKTNKKKNPTKKRKVNSEQEVTTVAAQ--DSLQQMDKLSSR-AVALESYYGTQQSV 762 (846)
T ss_pred cccCCccccccccccccCcCCccccccccccccCchhhhhhhhh--hhhhhHHhhhcc-cCCcccccccHHhh
Confidence 00001222221 34445444 788888887777777 33444 468899999998 58999999886544
No 2
>PF03101 FAR1: FAR1 DNA-binding domain; InterPro: IPR004330 Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. It has been found that the proteins governing this response, which include FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), are a pair of homologous proteins sharing significant sequence homology to mutator-like transposases. These proteins appear to be novel transcription factors, which are essential for activating the expression of FHY1 and FHL (for FHY1-like) and related genes, whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses in plants. The FRS (FAR1 Related Sequences) family of proteins share a similar domain structure to mutator-like transposases, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). It seems plausible that the FRS family represent transcription factors derived from mutator-like transposases [, ]. This entry represents a domain found in FAR1 and FRS proteins. It contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.
Probab=99.79 E-value=2.4e-19 Score=154.15 Aligned_cols=89 Identities=36% Similarity=0.651 Sum_probs=78.6
Q ss_pred HHHHHHhhhcCcEEEEecccccccCCceeEEEEEEccCCcccccccc-ccccccc-ccccCceeEEEEEEeeCceEEEEE
Q 046293 41 EFYKKYAKEGGFSIQINSSKICKESNDIIRKEYVCFKEGQARQSKVV-NRKRRRG-IIRGGCSANLVVVKYEFGKYMVRI 118 (695)
Q Consensus 41 ~~y~~yA~~~GF~i~~~~s~~~k~~g~~~~~~~~C~r~G~~~~~~~~-~~~r~~~-~~r~gC~a~i~~~~~~~~~w~v~~ 118 (695)
+||+.||..+||+|++.++++.+.+|.+++++|+|+++|.++.+... ...++++ +.++||||+|.+++..+|.|.|..
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~~~~w~v~~ 80 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRKDGKWRVTS 80 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEccCCEEEEEE
Confidence 59999999999999999998877789999999999999999886643 2344445 999999999999998899999999
Q ss_pred EeecccCCCCC
Q 046293 119 FVEEHNHTLSS 129 (695)
Q Consensus 119 ~~~~HNH~l~~ 129 (695)
++.+|||+|.+
T Consensus 81 ~~~~HNH~L~P 91 (91)
T PF03101_consen 81 FVLEHNHPLCP 91 (91)
T ss_pred CcCCcCCCCCC
Confidence 99999999863
No 3
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=99.70 E-value=3.4e-17 Score=141.39 Aligned_cols=79 Identities=39% Similarity=0.683 Sum_probs=75.5
Q ss_pred cccccCCCCCceee---EeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHHh--------
Q 046293 214 TTYNTNRYNMIFAP---FVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMIL-------- 282 (695)
Q Consensus 214 ~Ty~tn~y~~pL~~---~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~~-------- 282 (695)
+||+||+| +||+. ++|+|++|+.+|+||+++.+|+.++|.|+|+.|++.++.. |.+||||++.++.+
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~-p~~ii~D~~~~~~~Ai~~vfP~ 78 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQK-PKVIISDFDKALINAIKEVFPD 78 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccC-ceeeeccccHHHHHHHHHHCCC
Confidence 69999999 98886 9999999999999999999999999999999999999887 99999999999988
Q ss_pred ---hhhHHHHHHHHH
Q 046293 283 ---HLAYWHILNKFL 294 (695)
Q Consensus 283 ---~lC~~Hi~~n~~ 294 (695)
++|.||+.+|++
T Consensus 79 ~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 79 ARHQLCLFHILRNIK 93 (93)
T ss_pred ceEehhHHHHHHhhC
Confidence 999999999974
No 4
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=99.25 E-value=3.6e-11 Score=102.72 Aligned_cols=88 Identities=23% Similarity=0.343 Sum_probs=73.1
Q ss_pred cCCHHHHHHHHHHHhhhcCcEEEEecccccccCCceeEEEEEEccCCcccccccc--------------------ccc-c
Q 046293 33 FDTLDDAYEFYKKYAKEGGFSIQINSSKICKESNDIIRKEYVCFKEGQARQSKVV--------------------NRK-R 91 (695)
Q Consensus 33 F~S~eea~~~y~~yA~~~GF~i~~~~s~~~k~~g~~~~~~~~C~r~G~~~~~~~~--------------------~~~-r 91 (695)
|.+.+|...|++..+..+||.|++.+|.. ..+.|.|--+|.++.+... ... .
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~-------~ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~ 73 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDK-------KKIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKK 73 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCC-------ceEEEEEecCCCcccccccccccccccccccccccccccccccC
Confidence 89999999999999999999999999954 3589999998888764320 011 1
Q ss_pred ccc-ccccCceeEEEEEEee-CceEEEEEEeecccCCC
Q 046293 92 RRG-IIRGGCSANLVVVKYE-FGKYMVRIFVEEHNHTL 127 (695)
Q Consensus 92 ~~~-~~r~gC~a~i~~~~~~-~~~w~v~~~~~~HNH~l 127 (695)
+.. +..++|||+|++.... .+.|.|..++..|||||
T Consensus 74 k~t~srk~~CPFriRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 74 KRTKSRKNTCPFRIRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred CcccccccCCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence 222 7789999999999986 99999999999999986
No 5
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.93 E-value=4.5e-10 Score=72.98 Aligned_cols=26 Identities=42% Similarity=0.973 Sum_probs=24.7
Q ss_pred EeeecccccCCCchhhHHHHHHHcCc
Q 046293 473 SCICKKFKSEGIPCTHMLALFKKLQI 498 (695)
Q Consensus 473 tCsC~~~q~~GiPC~H~l~vl~~~~~ 498 (695)
+|+|++||.+||||+|+|+|+...++
T Consensus 2 ~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 2 TCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred cccCCCcccCCccHHHHHHHHHHhCC
Confidence 79999999999999999999999875
No 6
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=98.87 E-value=3.6e-10 Score=122.72 Aligned_cols=171 Identities=15% Similarity=0.173 Sum_probs=124.8
Q ss_pred cEEEEecccccCCC-----CCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHHh
Q 046293 208 DVIVFDTTYNTNRY-----NMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMIL 282 (695)
Q Consensus 208 dVl~iD~Ty~tn~y-----~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~~ 282 (695)
++|.+|++|.+-+. +..++.++|+|.+|+-.++|+.+...|+.++|.-+|+.|++- |-..|..||+|..+||..
T Consensus 163 ~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R-Gl~~~~lvv~Dg~~gl~~ 241 (381)
T PF00872_consen 163 PYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER-GLKDILLVVSDGHKGLKE 241 (381)
T ss_pred cceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc-cccccceeeccccccccc
Confidence 58999999987653 467899999999999999999999999999999999988753 224699999999999986
Q ss_pred -----------hhhHHHHHHHHHHhhhhhcccccHHHHHHHHhhcCChHHHHHHHHHHHHHhccchhHHHHHHHHh-hcc
Q 046293 283 -----------HLAYWHILNKFLERLSKTVHTENYRHFQKCIWESNTIEKFDALWKDVIDKAKLIENEWLQGVYEI-RSK 350 (695)
Q Consensus 283 -----------~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~~v~~~~t~~eFe~~w~~l~~~~~~~~~~~l~~l~~~-re~ 350 (695)
..|.+|+++|+.+++.......-..+++ .|+.+.+.++....++++.+++...-....+.|-.. .+.
T Consensus 242 ai~~~fp~a~~QrC~vH~~RNv~~~v~~k~~~~v~~~Lk-~I~~a~~~e~a~~~l~~f~~~~~~kyp~~~~~l~~~~~~~ 320 (381)
T PF00872_consen 242 AIREVFPGAKWQRCVVHLMRNVLRKVPKKDRKEVKADLK-AIYQAPDKEEAREALEEFAEKWEKKYPKAAKSLEENWDEL 320 (381)
T ss_pred cccccccchhhhhheechhhhhccccccccchhhhhhcc-ccccccccchhhhhhhhcccccccccchhhhhhhhccccc
Confidence 8999999999999985432211034443 467788899999989888776654333222221111 112
Q ss_pred chhhhhccccccCccccCcccchHHHHHHH
Q 046293 351 WVHAYVNHVFSAGMSSSNRAESNHAIFRRA 380 (695)
Q Consensus 351 Wa~ay~~~~~~~g~~tt~r~Es~n~~~~~~ 380 (695)
|+-.-+.....--+.|||.+||+|+.+++.
T Consensus 321 ~tf~~fP~~~~~~i~TTN~iEsln~~irrr 350 (381)
T PF00872_consen 321 LTFLDFPPEHRRSIRTTNAIESLNKEIRRR 350 (381)
T ss_pred cceeeecchhccccchhhhccccccchhhh
Confidence 222113333444678999999999887653
No 7
>PF03108 DBD_Tnp_Mut: MuDR family transposase; InterPro: IPR004332 The plant MuDR transposase domain is present in plant proteins that are presumed to be the transposases for Mutator transposable elements [, ]. The function of these proteins is unknown. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=98.73 E-value=5.2e-08 Score=78.27 Aligned_cols=66 Identities=21% Similarity=0.397 Sum_probs=57.1
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhhcCcEEEEecccccccCCceeEEEEEEccCCcccccccccccccccccccCceeE
Q 046293 24 NRKPHKGKKFDTLDDAYEFYKKYAKEGGFSIQINSSKICKESNDIIRKEYVCFKEGQARQSKVVNRKRRRGIIRGGCSAN 103 (695)
Q Consensus 24 ~~~p~~g~~F~S~eea~~~y~~yA~~~GF~i~~~~s~~~k~~g~~~~~~~~C~r~G~~~~~~~~~~~r~~~~~r~gC~a~ 103 (695)
++...+||+|+|.+|+..++..||..+||.++..++. ..++.++|... ||||+
T Consensus 1 n~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd-------~~r~~~~C~~~--------------------~C~Wr 53 (67)
T PF03108_consen 1 NPELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSD-------KKRYRAKCKDK--------------------GCPWR 53 (67)
T ss_pred CCccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccC-------CEEEEEEEcCC--------------------CCCEE
Confidence 3457899999999999999999999999999998883 45899999732 69999
Q ss_pred EEEEEee-CceEEE
Q 046293 104 LVVVKYE-FGKYMV 116 (695)
Q Consensus 104 i~~~~~~-~~~w~v 116 (695)
|+++..+ ++.|.|
T Consensus 54 v~as~~~~~~~~~I 67 (67)
T PF03108_consen 54 VRASKRKRSDTFQI 67 (67)
T ss_pred EEEEEcCCCCEEEC
Confidence 9999987 788875
No 8
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=98.26 E-value=7.6e-07 Score=63.53 Aligned_cols=28 Identities=36% Similarity=0.822 Sum_probs=25.7
Q ss_pred cceEEeeecccccCCCchhhHHHHHHHc
Q 046293 469 LDFVSCICKKFKSEGIPCTHMLALFKKL 496 (695)
Q Consensus 469 ~~~~tCsC~~~q~~GiPC~H~l~vl~~~ 496 (695)
....+|+|..|+..|.||+|+++|+...
T Consensus 12 ~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 12 IEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred ccccEeeCCCccccCCcchhHHHHHHhh
Confidence 5688999999999999999999999765
No 9
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=97.59 E-value=0.00035 Score=74.99 Aligned_cols=167 Identities=16% Similarity=0.173 Sum_probs=111.4
Q ss_pred cEEEEecccccCC--CCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHHh---
Q 046293 208 DVIVFDTTYNTNR--YNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMIL--- 282 (695)
Q Consensus 208 dVl~iD~Ty~tn~--y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~~--- 282 (695)
++|.+|++|.+-+ -+..++.++|++.+|+-.++|+-+-..|+ ..|.-+|..|..- +-..-..+++|...++.+
T Consensus 146 ~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~r-gl~~v~l~v~Dg~~gl~~aI~ 223 (379)
T COG3328 146 PYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNR-GLSDVLLVVVDGLKGLPEAIS 223 (379)
T ss_pred eEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhc-cccceeEEecchhhhhHHHHH
Confidence 5889999999887 46789999999999999999999999999 8888566556543 112345566799998876
Q ss_pred --------hhhHHHHHHHHHHhhhhhcccccHHHHHHHHhhcCChHHHHHHHHHHHHHhccch----hHHHHHHHHhhcc
Q 046293 283 --------HLAYWHILNKFLERLSKTVHTENYRHFQKCIWESNTIEKFDALWKDVIDKAKLIE----NEWLQGVYEIRSK 350 (695)
Q Consensus 283 --------~lC~~Hi~~n~~~~~~~~~~~~~~~~~~~~v~~~~t~~eFe~~w~~l~~~~~~~~----~~~l~~l~~~re~ 350 (695)
..|..|+.+|+..+......+. ...-.+.|+.+.+.++-...|..+...+...- ..|...+ . +.
T Consensus 224 ~v~p~a~~Q~C~vH~~Rnll~~v~~k~~d~-i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~yP~i~~~~~~~~-~--~~ 299 (379)
T COG3328 224 AVFPQAAVQRCIVHLVRNLLDKVPRKDQDA-VLSDLRSIYIAPDAEEALLALLAFSELWGKRYPAILKSWRNAL-E--EL 299 (379)
T ss_pred HhccHhhhhhhhhHHHhhhhhhhhhhhhHH-HHhhhhhhhccCCcHHHHHHHHHHHHhhhhhcchHHHHHHHHH-H--Hh
Confidence 8999999999998886542211 11222346778888888888888766443221 2222221 1 11
Q ss_pred chh-hhhccccccCccccCcccchHHHHHHHH
Q 046293 351 WVH-AYVNHVFSAGMSSSNRAESNHAIFRRAL 381 (695)
Q Consensus 351 Wa~-ay~~~~~~~g~~tt~r~Es~n~~~~~~l 381 (695)
|.- +|-+... .-+.|||-.|++|+.+....
T Consensus 300 ~~F~~fp~~~r-~~i~ttN~IE~~n~~ir~~~ 330 (379)
T COG3328 300 LPFFAFPSEIR-KIIYTTNAIESLNKLIRRRT 330 (379)
T ss_pred cccccCcHHHH-hHhhcchHHHHHHHHHHHHH
Confidence 110 1111111 23568999999998654443
No 10
>PF03106 WRKY: WRKY DNA -binding domain; InterPro: IPR003657 The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding []. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure []. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2AYD_A 1WJ2_A 2LEX_A.
Probab=93.36 E-value=0.39 Score=37.38 Aligned_cols=56 Identities=27% Similarity=0.385 Sum_probs=37.8
Q ss_pred cCcEEEEecccccccCCceeEEEEEEccCCcccccccccccccccccccCceeEEEEEEee-CceEEEEEEeecccCC
Q 046293 50 GGFSIQINSSKICKESNDIIRKEYVCFKEGQARQSKVVNRKRRRGIIRGGCSANLVVVKYE-FGKYMVRIFVEEHNHT 126 (695)
Q Consensus 50 ~GF~i~~~~s~~~k~~g~~~~~~~~C~r~G~~~~~~~~~~~r~~~~~r~gC~a~i~~~~~~-~~~w~v~~~~~~HNH~ 126 (695)
=||..|+--.+..+.+ ..-+..|.|+.. ||||.=.+.+.. ++.-.++....+|||+
T Consensus 3 Dgy~WRKYGqK~i~g~-~~pRsYYrCt~~--------------------~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 3 DGYRWRKYGQKNIKGS-PYPRSYYRCTHP--------------------GCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp SSS-EEEEEEEEETTT-TCEEEEEEEECT--------------------TEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CCCchhhccCcccCCC-ceeeEeeecccc--------------------ChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 3777776554333322 245678999753 799999998876 7888899999999996
No 11
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=93.32 E-value=0.044 Score=38.34 Aligned_cols=22 Identities=27% Similarity=0.842 Sum_probs=17.9
Q ss_pred ccCCCCCCCCCCCCC--CCCcchhhh
Q 046293 631 RRCNGCGLVGQSHDK--RNCPLLIKR 654 (695)
Q Consensus 631 ~~C~~C~~~~~GHn~--~tCp~~~~~ 654 (695)
++|+.|| +.||.+ ++||+....
T Consensus 2 ~kC~~CG--~~GH~~t~k~CP~~~~~ 25 (40)
T PF15288_consen 2 VKCKNCG--AFGHMRTNKRCPMYCWS 25 (40)
T ss_pred ccccccc--cccccccCccCCCCCCC
Confidence 6899999 679954 899997653
No 12
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=93.28 E-value=0.065 Score=30.85 Aligned_cols=18 Identities=44% Similarity=1.099 Sum_probs=15.9
Q ss_pred ccCCCCCCCCCCCCCCCCcc
Q 046293 631 RRCNGCGLVGQSHDKRNCPL 650 (695)
Q Consensus 631 ~~C~~C~~~~~GHn~~tCp~ 650 (695)
+.|-+|+ ..||.++.||+
T Consensus 1 ~~C~~C~--~~GH~~~~Cp~ 18 (18)
T PF00098_consen 1 RKCFNCG--EPGHIARDCPK 18 (18)
T ss_dssp SBCTTTS--CSSSCGCTSSS
T ss_pred CcCcCCC--CcCcccccCcc
Confidence 4799999 68999999995
No 13
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=89.58 E-value=1.9 Score=38.13 Aligned_cols=75 Identities=21% Similarity=0.187 Sum_probs=55.0
Q ss_pred CcEEEEeccccc-CCCCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHHh
Q 046293 207 GDVIVFDTTYNT-NRYNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMIL 282 (695)
Q Consensus 207 ~dVl~iD~Ty~t-n~y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~~ 282 (695)
+.++.+|.+... ...++....++.+|..-.. ++++.+-..++.+.+.-+|.......++..|.+|+||+..+...
T Consensus 6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSRF-IYAFPVSSKETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFTS 81 (120)
T ss_dssp TTEEEEEEEEETGGCTT-CEEEEEEEETTTTE-EEEEEESSSSHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHHS
T ss_pred CCEEEEeeEEEecCCCCccEEEEEEEECCCCc-EEEEEeecccccccccccccccccccccccceeccccccccccc
Confidence 467888888544 3445578888888887654 45777777778888888888777777665599999999999865
No 14
>PF04684 BAF1_ABF1: BAF1 / ABF1 chromatin reorganising factor; InterPro: IPR006774 ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture []. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 Saccharomyces cerevisiae (P14164 from SWISSPROT)) []. The N-terminal two thirds of the protein are necessary for DNA binding, and the N terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilise the protein structure [].; GO: 0003677 DNA binding, 0006338 chromatin remodeling, 0005634 nucleus
Probab=86.43 E-value=1.5 Score=47.39 Aligned_cols=56 Identities=20% Similarity=0.407 Sum_probs=47.8
Q ss_pred CCCccCCHHHHHHHHHHHhhhcCcEEEEecccccccCCceeEEEEEEccCCcccccccccccccccccccCceeEEEEEE
Q 046293 29 KGKKFDTLDDAYEFYKKYAKEGGFSIQINSSKICKESNDIIRKEYVCFKEGQARQSKVVNRKRRRGIIRGGCSANLVVVK 108 (695)
Q Consensus 29 ~g~~F~S~eea~~~y~~yA~~~GF~i~~~~s~~~k~~g~~~~~~~~C~r~G~~~~~~~~~~~r~~~~~r~gC~a~i~~~~ 108 (695)
-+..|+++++-|+.+|.|......-|+...|.+.| -.+|.|..- +|||+|.+..
T Consensus 24 ~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nk------hftfachlk--------------------~c~fkillsy 77 (496)
T PF04684_consen 24 QARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNK------HFTFACHLK--------------------NCPFKILLSY 77 (496)
T ss_pred cccCCCcHHHHHHHHhhhhhhhcCceeeccccccc------ceEEEeecc--------------------CCCceeeeee
Confidence 36789999999999999999999999998886554 589999863 6999999987
Q ss_pred ee
Q 046293 109 YE 110 (695)
Q Consensus 109 ~~ 110 (695)
.+
T Consensus 78 ~g 79 (496)
T PF04684_consen 78 CG 79 (496)
T ss_pred cc
Confidence 64
No 15
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=85.03 E-value=0.49 Score=52.46 Aligned_cols=28 Identities=32% Similarity=0.816 Sum_probs=22.4
Q ss_pred cCCCCcccCCCCCCCCCCC--CCCCCcchhhh
Q 046293 625 KGKDKGRRCNGCGLVGQSH--DKRNCPLLIKR 654 (695)
Q Consensus 625 ~~~kr~~~C~~C~~~~~GH--n~~tCp~~~~~ 654 (695)
|+|..+++|+.|||+ || +-..||+....
T Consensus 932 GRK~Ttr~C~nCGQv--GHmkTNK~CP~f~s~ 961 (968)
T COG5179 932 GRKNTTRTCGNCGQV--GHMKTNKACPKFSSK 961 (968)
T ss_pred CCCCcceeccccccc--ccccccccCccccCC
Confidence 446678999999975 99 66789998764
No 16
>smart00774 WRKY DNA binding domain. The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding.
Probab=84.15 E-value=2.2 Score=32.95 Aligned_cols=55 Identities=25% Similarity=0.380 Sum_probs=36.7
Q ss_pred CcEEEEecccccccCCceeEEEEEEccCCcccccccccccccccccccCceeEEEEEEee-CceEEEEEEeecccC
Q 046293 51 GFSIQINSSKICKESNDIIRKEYVCFKEGQARQSKVVNRKRRRGIIRGGCSANLVVVKYE-FGKYMVRIFVEEHNH 125 (695)
Q Consensus 51 GF~i~~~~s~~~k~~g~~~~~~~~C~r~G~~~~~~~~~~~r~~~~~r~gC~a~i~~~~~~-~~~w~v~~~~~~HNH 125 (695)
||..|+=-.+..+.+ .--+..|.|+.. .||||+=.|.+.. ++.-.++.+..+|||
T Consensus 4 Gy~WRKYGQK~ikgs-~~pRsYYrCt~~-------------------~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 4 GYQWRKYGQKVIKGS-PFPRSYYRCTYS-------------------QGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cccccccCcEecCCC-cCcceEEecccc-------------------CCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 566665433322222 234567888761 2799988787765 788888899999998
No 17
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=83.36 E-value=0.56 Score=31.26 Aligned_cols=23 Identities=30% Similarity=0.686 Sum_probs=19.4
Q ss_pred CCcccCCCCCCCCCCCCCCCCcchh
Q 046293 628 DKGRRCNGCGLVGQSHDKRNCPLLI 652 (695)
Q Consensus 628 kr~~~C~~C~~~~~GHn~~tCp~~~ 652 (695)
...+.|.+|+ ..||-++.||.++
T Consensus 6 P~~Y~C~~C~--~~GH~i~dCP~~~ 28 (32)
T PF13696_consen 6 PPGYVCHRCG--QKGHWIQDCPTNK 28 (32)
T ss_pred CCCCEeecCC--CCCccHhHCCCCC
Confidence 3568999999 6799999999854
No 18
>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.
Probab=77.44 E-value=3.8 Score=31.49 Aligned_cols=25 Identities=40% Similarity=0.477 Sum_probs=10.7
Q ss_pred cCceeEEEEEEeeCceEEEEEEeecccC
Q 046293 98 GGCSANLVVVKYEFGKYMVRIFVEEHNH 125 (695)
Q Consensus 98 ~gC~a~i~~~~~~~~~w~v~~~~~~HNH 125 (695)
.+|+|.+.+. .+.-.+.....+|||
T Consensus 38 ~~C~a~~~~~---~~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 38 HGCRARLITD---AGDGRVVRTNGEHNH 62 (62)
T ss_dssp S----EEEEE-----TTEEEE-S---SS
T ss_pred CCCeEEEEEE---CCCCEEEECCCccCC
Confidence 4799999997 233456666689999
No 19
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=67.00 E-value=2.4 Score=31.47 Aligned_cols=20 Identities=35% Similarity=0.800 Sum_probs=17.3
Q ss_pred CcccCCCCCCCCCCCCCCCCcc
Q 046293 629 KGRRCNGCGLVGQSHDKRNCPL 650 (695)
Q Consensus 629 r~~~C~~C~~~~~GHn~~tCp~ 650 (695)
-...|..|+ ..||+.+.||+
T Consensus 30 lp~~C~~C~--~~gH~~~~C~k 49 (49)
T PF14392_consen 30 LPRFCFHCG--RIGHSDKECPK 49 (49)
T ss_pred cChhhcCCC--CcCcCHhHcCC
Confidence 457999999 67999999985
No 20
>smart00343 ZnF_C2HC zinc finger.
Probab=66.94 E-value=3.1 Score=26.25 Aligned_cols=18 Identities=39% Similarity=1.066 Sum_probs=15.4
Q ss_pred cCCCCCCCCCCCCCCCCcch
Q 046293 632 RCNGCGLVGQSHDKRNCPLL 651 (695)
Q Consensus 632 ~C~~C~~~~~GHn~~tCp~~ 651 (695)
.|.+|+ ..||..+.||..
T Consensus 1 ~C~~CG--~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCG--KEGHIARDCPKX 18 (26)
T ss_pred CCccCC--CCCcchhhCCcc
Confidence 489999 689999999944
No 21
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=65.54 E-value=1.9 Score=39.89 Aligned_cols=70 Identities=20% Similarity=0.297 Sum_probs=54.1
Q ss_pred CcEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHH
Q 046293 207 GDVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAM 280 (695)
Q Consensus 207 ~dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al 280 (695)
|+.+.+|-||.+-+ +--.+....+|.+++ ++++-|-..-+...=..||..+++..+ ..|.+|+||..++.
T Consensus 1 ~~~w~~DEt~iki~-G~~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~-~~p~~ivtDk~~aY 70 (140)
T PF13610_consen 1 GDSWHVDETYIKIK-GKWHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-GEPRVIVTDKLPAY 70 (140)
T ss_pred CCEEEEeeEEEEEC-CEEEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-cccceeecccCCcc
Confidence 57889999997643 224556788999998 778878777787777778777776665 68999999997764
No 22
>PHA02517 putative transposase OrfB; Reviewed
Probab=60.96 E-value=34 Score=35.30 Aligned_cols=74 Identities=18% Similarity=0.030 Sum_probs=47.6
Q ss_pred CcEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHHHh
Q 046293 207 GDVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAMIL 282 (695)
Q Consensus 207 ~dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al~~ 282 (695)
..++..|-||..... +-.+.++.+|...+ .++|+.+...++.+...-+|+......+.+.+..|.||+......
T Consensus 110 n~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~~l~~a~~~~~~~~~~i~~sD~G~~y~s 183 (277)
T PHA02517 110 NQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLDALEQALWARGRPGGLIHHSDKGSQYVS 183 (277)
T ss_pred CCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHHHHHHHHHHHhcCCCcCcEeecccccccch
Confidence 468999999975443 34566666777655 456788877777775544444444444433345677999887543
No 23
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=53.72 E-value=1.5e+02 Score=27.80 Aligned_cols=97 Identities=22% Similarity=0.253 Sum_probs=65.8
Q ss_pred hHHHhhCCcEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccC--CChhhHHHHHHHHHHHCCCCCCceeecCCh
Q 046293 200 RRAYKFYGDVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSD--ETTESFLWLFEQFKEAMPGDDPKMIITDQD 277 (695)
Q Consensus 200 ~~~~~~f~dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~--E~~es~~W~l~~f~~~~~~~~p~~iitD~~ 277 (695)
+..+..+|--|..|+= ++..+.+|+.|+.....|-.|+-.. -.++ .+.+.+.-+++...+-+|...-..||||-.
T Consensus 26 k~~w~~~Gcsi~~DgW--td~~~~~lInf~v~~~~g~~Flksv-d~s~~~~~a~~l~~ll~~vIeeVG~~nVvqVVTDn~ 102 (153)
T PF04937_consen 26 KKSWKRTGCSIMSDGW--TDRKGRSLINFMVYCPEGTVFLKSV-DASSIIKTAEYLFELLDEVIEEVGEENVVQVVTDNA 102 (153)
T ss_pred HHHHHhcCEEEEEecC--cCCCCCeEEEEEEEcccccEEEEEE-ecccccccHHHHHHHHHHHHHHhhhhhhhHHhccCc
Confidence 4455666766777775 5667778888887777666554332 2222 356666666666666677667777899999
Q ss_pred HHHHh--------------hhhHHHHHHHHHHhhhh
Q 046293 278 PAMIL--------------HLAYWHILNKFLERLSK 299 (695)
Q Consensus 278 ~al~~--------------~lC~~Hi~~n~~~~~~~ 299 (695)
..+.+ ..|..|-+.-+.+.+..
T Consensus 103 ~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 103 SNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred hhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 88766 56777777777777654
No 24
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=37.65 E-value=1.3e+02 Score=30.87 Aligned_cols=72 Identities=8% Similarity=-0.068 Sum_probs=49.4
Q ss_pred CcEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccC-CChhhHHHHHHHHHHHC-C---CCCCceeecCChHH
Q 046293 207 GDVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSD-ETTESFLWLFEQFKEAM-P---GDDPKMIITDQDPA 279 (695)
Q Consensus 207 ~dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~-E~~es~~W~l~~f~~~~-~---~~~p~~iitD~~~a 279 (695)
..|.+.|-||....-+.-++..+.+|.+.. .++|+++-.. .+.+...-+|+..+... + ...|..|.||+...
T Consensus 87 n~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~~l~~A~~~~~~~~~~~~~~iihSD~Gsq 163 (262)
T PRK14702 87 NQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSC 163 (262)
T ss_pred CCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHHHHHHHHHHHhcccCCCCCeEEEcCCCcc
Confidence 368999999876544546788888888876 6679998764 56665555555444332 2 23578899999654
No 25
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=34.70 E-value=1.7e+02 Score=30.79 Aligned_cols=72 Identities=8% Similarity=-0.043 Sum_probs=49.9
Q ss_pred CcEEEEecccccCCCCCceeeEeEEecCCceEEEEEEeccC-CChhhHHHHHHHHHHH-CCC---CCCceeecCChHH
Q 046293 207 GDVIVFDTTYNTNRYNMIFAPFVGVNNHGQTIIFGCGFLSD-ETTESFLWLFEQFKEA-MPG---DDPKMIITDQDPA 279 (695)
Q Consensus 207 ~dVl~iD~Ty~tn~y~~pL~~~~g~d~~~~~~~~~~al~~~-E~~es~~W~l~~f~~~-~~~---~~p~~iitD~~~a 279 (695)
..|.+.|-||....-+.-++.++.+|.... .++|+++-.. .+.+...-+|+..+.. .+. ..|..|.||+...
T Consensus 126 N~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGsq 202 (301)
T PRK09409 126 NQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSC 202 (301)
T ss_pred CCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCcc
Confidence 469999999965544445778888888877 6789999875 5666666666543333 332 3577889999654
No 26
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=34.69 E-value=26 Score=25.14 Aligned_cols=19 Identities=37% Similarity=0.840 Sum_probs=17.0
Q ss_pred cccCCCCCCCCCCCCCCCCcc
Q 046293 630 GRRCNGCGLVGQSHDKRNCPL 650 (695)
Q Consensus 630 ~~~C~~C~~~~~GHn~~tCp~ 650 (695)
...|.+|+ ..||-..-||+
T Consensus 4 ~~~CqkC~--~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCG--QKGHWTYECPN 22 (42)
T ss_pred CCcCcccC--CCCcchhhCCC
Confidence 46899999 68999999996
No 27
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=34.33 E-value=22 Score=35.77 Aligned_cols=24 Identities=29% Similarity=0.779 Sum_probs=19.9
Q ss_pred eEEeeecccccCCCchhhHHHHHHHcC
Q 046293 471 FVSCICKKFKSEGIPCTHMLALFKKLQ 497 (695)
Q Consensus 471 ~~tCsC~~~q~~GiPC~H~l~vl~~~~ 497 (695)
..-|||--|. .||.||-+|..++.
T Consensus 124 ~~dCSCPD~a---nPCKHi~AvyY~la 147 (266)
T COG4279 124 STDCSCPDYA---NPCKHIAAVYYLLA 147 (266)
T ss_pred ccccCCCCcc---cchHHHHHHHHHHH
Confidence 4469999875 69999999998874
No 28
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=29.12 E-value=26 Score=37.50 Aligned_cols=24 Identities=33% Similarity=0.771 Sum_probs=21.0
Q ss_pred CcccCCCCCCCCCCCCCCCCcchhhh
Q 046293 629 KGRRCNGCGLVGQSHDKRNCPLLIKR 654 (695)
Q Consensus 629 r~~~C~~C~~~~~GHn~~tCp~~~~~ 654 (695)
...-|.+|+ |.||...-||++...
T Consensus 569 ~~kGCayCg--GLGHRItdCPKle~~ 592 (610)
T KOG0341|consen 569 GEKGCAYCG--GLGHRITDCPKLEAQ 592 (610)
T ss_pred Ccccccccc--CCCcccccCchhhhh
Confidence 345899999 999999999999875
No 29
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=26.99 E-value=58 Score=28.10 Aligned_cols=27 Identities=30% Similarity=0.690 Sum_probs=19.5
Q ss_pred EEEEEecCcceEEeeeccccc----CC-CchhhHHHHH
Q 046293 461 FEVLYDKKLDFVSCICKKFKS----EG-IPCTHMLALF 493 (695)
Q Consensus 461 ~~V~~d~~~~~~tCsC~~~q~----~G-iPC~H~l~vl 493 (695)
|+++. ..|||..|-. -| -||.|++.+=
T Consensus 45 YIl~~------gfCSCp~~~~svvl~Gk~~C~Hi~glk 76 (117)
T COG5431 45 YILEG------GFCSCPDFLGSVVLKGKSPCAHIIGLK 76 (117)
T ss_pred eEEEc------CcccCHHHHhHhhhcCcccchhhhhee
Confidence 88864 3899999872 23 4699998753
No 30
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=26.64 E-value=1.1e+02 Score=30.79 Aligned_cols=85 Identities=16% Similarity=0.152 Sum_probs=53.8
Q ss_pred EEEecccccCCCCCceeeEeEEec--CCceEEEEEEeccCCChhhHHHHHHHH-HHHCCCCCCceeecCChHHHHh----
Q 046293 210 IVFDTTYNTNRYNMIFAPFVGVNN--HGQTIIFGCGFLSDETTESFLWLFEQF-KEAMPGDDPKMIITDQDPAMIL---- 282 (695)
Q Consensus 210 l~iD~Ty~tn~y~~pL~~~~g~d~--~~~~~~~~~al~~~E~~es~~W~l~~f-~~~~~~~~p~~iitD~~~al~~---- 282 (695)
|+||=+.......- +..+.+|. ++..++ .++.+-+.+++.-+|..+ -.. ......+|++|..++...
T Consensus 1 lgiDE~~~~~g~~~--y~t~~~d~~~~~~~il---~i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~ 74 (249)
T PF01610_consen 1 LGIDEFAFRKGHRS--YVTVVVDLDTDTGRIL---DILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIRE 74 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCceEE---EEcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCccccccccc
Confidence 35565544332221 33444555 333333 478888888877777655 222 335778999999998766
Q ss_pred -------hhhHHHHHHHHHHhhhhh
Q 046293 283 -------HLAYWHILNKFLERLSKT 300 (695)
Q Consensus 283 -------~lC~~Hi~~n~~~~~~~~ 300 (695)
.+-.|||++++.+.+...
T Consensus 75 ~~P~A~iv~DrFHvvk~~~~al~~v 99 (249)
T PF01610_consen 75 YFPNAQIVADRFHVVKLANRALDKV 99 (249)
T ss_pred cccccccccccchhhhhhhhcchhh
Confidence 455799999998876543
No 31
>PF11433 DUF3198: Protein of unknown function (DUF3198); InterPro: IPR024504 This domain is found at the C-terminal of a family of archaeal proteins annotated as membrane proteins.; PDB: 1X9B_A.
Probab=25.47 E-value=1.7e+02 Score=21.47 Aligned_cols=44 Identities=18% Similarity=0.299 Sum_probs=28.0
Q ss_pred HHHHHHhhcCChHHHHHHHHHHHHHhccchhHHHHHHHHhhccch
Q 046293 308 HFQKCIWESNTIEKFDALWKDVIDKAKLIENEWLQGVYEIRSKWV 352 (695)
Q Consensus 308 ~~~~~v~~~~t~~eFe~~w~~l~~~~~~~~~~~l~~l~~~re~Wa 352 (695)
.|...| ++++..+|-....+|...-.--+..|...+-+.+++|-
T Consensus 6 ~Fe~~I-nS~SK~~Fv~nL~ELE~is~rlg~~Y~~~LeeaK~kWk 49 (51)
T PF11433_consen 6 KFESYI-NSESKSVFVRNLTELERISKRLGKSYQIRLEEAKEKWK 49 (51)
T ss_dssp HHHHHH-HS--HHHHHHHHHHHHHHHHHH-SHHHHHHHHHHHHH-
T ss_pred HHHHHh-CCccHHHHHHhHHHHHHHHHHHchHHHHHHHHHHHhhc
Confidence 566655 48888999888888754322224678877888889984
No 32
>PF12762 DDE_Tnp_IS1595: ISXO2-like transposase domain; InterPro: IPR024445 This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.
Probab=23.92 E-value=2.1e+02 Score=26.33 Aligned_cols=50 Identities=22% Similarity=0.157 Sum_probs=28.9
Q ss_pred eeEeEEecC-CceEEEEEEeccCCChhhHHHHHHHHHHHCCCCCCceeecCChHHH
Q 046293 226 APFVGVNNH-GQTIIFGCGFLSDETTESFLWLFEQFKEAMPGDDPKMIITDQDPAM 280 (695)
Q Consensus 226 ~~~~g~d~~-~~~~~~~~al~~~E~~es~~W~l~~f~~~~~~~~p~~iitD~~~al 280 (695)
..+++++-. +.+--+...++.+.+.+++.=+++... .+..+|+||...+-
T Consensus 36 ~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~~~i-----~~gs~i~TD~~~aY 86 (151)
T PF12762_consen 36 PVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQEHI-----EPGSTIITDGWRAY 86 (151)
T ss_pred EEEEEEeecccCCceEEEEeecccccchhHHHHHHhh-----hccceeeecchhhc
Confidence 334444444 333344445567788887755554333 23477899997764
No 33
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=22.65 E-value=75 Score=27.60 Aligned_cols=28 Identities=32% Similarity=0.599 Sum_probs=21.8
Q ss_pred CCCccCCHHHHHHHHHHHhhhcCcEEEEeccc
Q 046293 29 KGKKFDTLDDAYEFYKKYAKEGGFSIQINSSK 60 (695)
Q Consensus 29 ~g~~F~S~eea~~~y~~yA~~~GF~i~~~~s~ 60 (695)
+.+.|+|.|+|.. ||.++|....+.-..
T Consensus 51 v~l~F~skE~Ai~----yaer~G~~Y~V~~p~ 78 (101)
T PF04800_consen 51 VRLKFDSKEDAIA----YAERNGWDYEVEEPK 78 (101)
T ss_dssp CEEEESSHHHHHH----HHHHCT-EEEEE-ST
T ss_pred eEeeeCCHHHHHH----HHHHcCCeEEEeCCC
Confidence 7789999999975 789999998877553
No 34
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=21.09 E-value=33 Score=26.16 Aligned_cols=21 Identities=29% Similarity=0.694 Sum_probs=8.0
Q ss_pred CcccCCCCCCCCC---CCCCCCCcch
Q 046293 629 KGRRCNGCGLVGQ---SHDKRNCPLL 651 (695)
Q Consensus 629 r~~~C~~C~~~~~---GHn~~tCp~~ 651 (695)
|.+.|..|| .+ .|+.+=||++
T Consensus 32 r~y~Cp~Cg--AtGd~AHT~~yCP~k 55 (55)
T PF05741_consen 32 RKYVCPICG--ATGDNAHTIKYCPKK 55 (55)
T ss_dssp GG---TTT-----GGG---GGG-TT-
T ss_pred hcCcCCCCc--CcCccccccccCcCC
Confidence 568999999 64 5777778863
No 35
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=20.98 E-value=2.5e+02 Score=22.89 Aligned_cols=28 Identities=25% Similarity=0.400 Sum_probs=24.7
Q ss_pred ccCCHHHHHHHHHHHhhhcCcEEEEecc
Q 046293 32 KFDTLDDAYEFYKKYAKEGGFSIQINSS 59 (695)
Q Consensus 32 ~F~S~eea~~~y~~yA~~~GF~i~~~~s 59 (695)
.|+|.++....+..||.++|-....-.-
T Consensus 13 ~yPs~e~i~~aIE~YC~~~~~~l~Fisr 40 (74)
T PF14201_consen 13 KYPSKEEICEAIEKYCIKNGESLEFISR 40 (74)
T ss_pred CCCCHHHHHHHHHHHHHHcCCceEEEec
Confidence 5889999999999999999999986643
Done!